Multiple sequence alignment - TraesCS1D01G195400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G195400 chr1D 100.000 3059 0 0 1 3059 274468251 274465193 0.000000e+00 5650.0
1 TraesCS1D01G195400 chr1D 96.964 527 8 3 1151 1675 442449993 442450513 0.000000e+00 878.0
2 TraesCS1D01G195400 chr1D 99.287 421 3 0 1151 1571 430066948 430066528 0.000000e+00 761.0
3 TraesCS1D01G195400 chr1D 94.898 98 3 2 1580 1675 430066222 430066125 5.280000e-33 152.0
4 TraesCS1D01G195400 chr1A 91.451 2281 82 51 2 2223 347322274 347320048 0.000000e+00 3027.0
5 TraesCS1D01G195400 chr1A 80.297 472 52 24 2598 3058 347319267 347318826 4.920000e-83 318.0
6 TraesCS1D01G195400 chr1B 93.178 1759 63 23 490 2224 374017735 374016010 0.000000e+00 2531.0
7 TraesCS1D01G195400 chr1B 92.527 455 28 5 2 454 374018174 374017724 0.000000e+00 647.0
8 TraesCS1D01G195400 chr1B 88.664 247 23 5 2816 3058 374008715 374008470 2.310000e-76 296.0
9 TraesCS1D01G195400 chr1B 100.000 32 0 0 2217 2248 374016004 374015973 3.290000e-05 60.2
10 TraesCS1D01G195400 chr7D 100.000 28 0 0 820 847 496167084 496167111 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G195400 chr1D 274465193 274468251 3058 True 5650.0 5650 100.0000 1 3059 1 chr1D.!!$R1 3058
1 TraesCS1D01G195400 chr1D 442449993 442450513 520 False 878.0 878 96.9640 1151 1675 1 chr1D.!!$F1 524
2 TraesCS1D01G195400 chr1D 430066125 430066948 823 True 456.5 761 97.0925 1151 1675 2 chr1D.!!$R2 524
3 TraesCS1D01G195400 chr1A 347318826 347322274 3448 True 1672.5 3027 85.8740 2 3058 2 chr1A.!!$R1 3056
4 TraesCS1D01G195400 chr1B 374015973 374018174 2201 True 1079.4 2531 95.2350 2 2248 3 chr1B.!!$R2 2246

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
485 487 0.039035 GATAGTTGGGTGGGGTTGCA 59.961 55.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 3295 0.320374 TGCTAGGAACAACGTCCCAG 59.68 55.0 0.0 0.0 38.59 4.45 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.612453 TGGCAGCAATGGCAGAATCA 60.612 50.000 0.00 0.00 44.61 2.57
62 63 7.885922 TGGTGATAATAAAGGTTGAGCTTTACA 59.114 33.333 15.26 8.06 0.00 2.41
73 74 1.536766 GAGCTTTACATGTGCTGTGCA 59.463 47.619 13.39 0.00 38.92 4.57
81 82 1.034356 ATGTGCTGTGCATGTGTGTT 58.966 45.000 0.00 0.00 41.91 3.32
97 98 1.726791 GTGTTATGTGTGGAGTGAGCG 59.273 52.381 0.00 0.00 0.00 5.03
170 171 2.355126 CATCCGACGGCGATCCAG 60.355 66.667 15.16 0.00 40.82 3.86
224 226 0.459237 TGCGCCTTTGTGGTTTGTTG 60.459 50.000 4.18 0.00 38.35 3.33
352 354 5.178438 GTGGTGTGTTCTCTTCTCATCTTTC 59.822 44.000 0.00 0.00 0.00 2.62
357 359 7.440856 GTGTGTTCTCTTCTCATCTTTCTTCTT 59.559 37.037 0.00 0.00 0.00 2.52
358 360 7.989741 TGTGTTCTCTTCTCATCTTTCTTCTTT 59.010 33.333 0.00 0.00 0.00 2.52
364 366 6.933521 TCTTCTCATCTTTCTTCTTTGTGGAG 59.066 38.462 0.00 0.00 0.00 3.86
378 380 2.190578 GGAGGGGCGGATTGAGTG 59.809 66.667 0.00 0.00 0.00 3.51
404 406 1.438651 CATTTCGCCTCGGAGTCAAA 58.561 50.000 4.02 0.55 0.00 2.69
419 421 4.870991 GGAGTCAAAGGTAATTCTCTTCCG 59.129 45.833 0.00 0.00 0.00 4.30
423 425 6.771267 AGTCAAAGGTAATTCTCTTCCGTTTT 59.229 34.615 0.00 0.00 0.00 2.43
446 448 0.674581 CTGTGAATGCCCGCTCTTCA 60.675 55.000 2.45 2.45 0.00 3.02
454 456 0.379669 GCCCGCTCTTCATGTTCATG 59.620 55.000 6.46 6.46 0.00 3.07
463 465 1.441738 TCATGTTCATGTGCAGACCG 58.558 50.000 11.73 0.00 0.00 4.79
468 470 0.324614 TTCATGTGCAGACCGTGGAT 59.675 50.000 0.00 0.00 0.00 3.41
473 475 1.337728 TGTGCAGACCGTGGATAGTTG 60.338 52.381 0.00 0.00 0.00 3.16
476 478 0.902531 CAGACCGTGGATAGTTGGGT 59.097 55.000 0.00 0.00 0.00 4.51
477 479 0.902531 AGACCGTGGATAGTTGGGTG 59.097 55.000 0.00 0.00 0.00 4.61
478 480 0.107848 GACCGTGGATAGTTGGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
479 481 1.223487 CCGTGGATAGTTGGGTGGG 59.777 63.158 0.00 0.00 0.00 4.61
480 482 1.223487 CGTGGATAGTTGGGTGGGG 59.777 63.158 0.00 0.00 0.00 4.96
482 484 0.702316 GTGGATAGTTGGGTGGGGTT 59.298 55.000 0.00 0.00 0.00 4.11
483 485 0.701731 TGGATAGTTGGGTGGGGTTG 59.298 55.000 0.00 0.00 0.00 3.77
484 486 0.683179 GGATAGTTGGGTGGGGTTGC 60.683 60.000 0.00 0.00 0.00 4.17
485 487 0.039035 GATAGTTGGGTGGGGTTGCA 59.961 55.000 0.00 0.00 0.00 4.08
487 489 1.357272 TAGTTGGGTGGGGTTGCAGT 61.357 55.000 0.00 0.00 0.00 4.40
559 589 2.486982 CCTTGTGATTCTTGAGGCACAG 59.513 50.000 0.00 0.00 41.63 3.66
666 710 2.477375 TGATACGGTTGAAACTTGTCGC 59.523 45.455 0.00 0.00 0.00 5.19
675 719 2.089433 AAACTTGTCGCGCGTCTGTG 62.089 55.000 30.98 18.91 0.00 3.66
693 739 7.587629 CGTCTGTGGTTTATATATTCTCGGTA 58.412 38.462 0.00 0.00 0.00 4.02
795 846 0.104409 GGGGGACAGGGGATACAGAT 60.104 60.000 0.00 0.00 39.74 2.90
800 851 4.450265 GGGGACAGGGGATACAGATAAGTA 60.450 50.000 0.00 0.00 39.74 2.24
866 917 2.048127 GGTTTCGCTCTCGCCAGT 60.048 61.111 0.00 0.00 35.26 4.00
873 924 1.576421 GCTCTCGCCAGTGGTTTTG 59.424 57.895 11.74 0.00 0.00 2.44
889 940 4.220382 TGGTTTTGGCATAGAGATTTGTGG 59.780 41.667 0.00 0.00 0.00 4.17
903 954 4.487412 GTGGCGATGCTGCAAGGC 62.487 66.667 21.81 21.81 36.28 4.35
959 1010 3.146066 CAGGATCTTTTCCCGTCAAACA 58.854 45.455 0.00 0.00 46.81 2.83
1080 1140 0.828677 AGGAAACTAACCGGGATCCG 59.171 55.000 6.32 0.86 43.43 4.18
2062 2429 3.541713 GGTCCCTGCTCTAGGCGG 61.542 72.222 5.34 5.34 45.89 6.13
2083 2450 2.985847 GCGGGCTGCCTTGTTTCT 60.986 61.111 19.68 0.00 37.76 2.52
2084 2451 1.674322 GCGGGCTGCCTTGTTTCTA 60.674 57.895 19.68 0.00 37.76 2.10
2085 2452 1.923227 GCGGGCTGCCTTGTTTCTAC 61.923 60.000 19.68 0.00 37.76 2.59
2086 2453 0.605319 CGGGCTGCCTTGTTTCTACA 60.605 55.000 19.68 0.00 0.00 2.74
2087 2454 0.881796 GGGCTGCCTTGTTTCTACAC 59.118 55.000 19.68 0.00 32.98 2.90
2088 2455 1.604604 GGCTGCCTTGTTTCTACACA 58.395 50.000 12.43 0.00 32.98 3.72
2089 2456 2.162681 GGCTGCCTTGTTTCTACACAT 58.837 47.619 12.43 0.00 32.98 3.21
2090 2457 2.095059 GGCTGCCTTGTTTCTACACATG 60.095 50.000 12.43 0.00 32.98 3.21
2091 2458 2.095059 GCTGCCTTGTTTCTACACATGG 60.095 50.000 0.00 2.18 42.41 3.66
2092 2459 3.411446 CTGCCTTGTTTCTACACATGGA 58.589 45.455 9.35 0.00 42.21 3.41
2093 2460 4.012374 CTGCCTTGTTTCTACACATGGAT 58.988 43.478 9.35 0.00 42.21 3.41
2094 2461 4.009675 TGCCTTGTTTCTACACATGGATC 58.990 43.478 9.35 0.00 42.21 3.36
2126 2493 2.434702 ACTTCGTTCTTGTTCCTCCACT 59.565 45.455 0.00 0.00 0.00 4.00
2150 2517 4.607955 TGATGATTCAGTTATCGTCGTCC 58.392 43.478 0.00 0.00 41.43 4.79
2161 2528 2.567049 GTCGTCCGGACAGTCCTG 59.433 66.667 32.80 16.26 45.36 3.86
2209 2578 5.201910 TGTGTGTGAATCGAACGAAATTTC 58.798 37.500 8.20 8.20 0.00 2.17
2210 2579 5.201910 GTGTGTGAATCGAACGAAATTTCA 58.798 37.500 17.99 4.54 0.00 2.69
2211 2580 5.851177 GTGTGTGAATCGAACGAAATTTCAT 59.149 36.000 17.99 6.12 0.00 2.57
2213 2582 6.577055 TGTGTGAATCGAACGAAATTTCATTC 59.423 34.615 15.30 15.30 0.00 2.67
2215 2584 6.072728 TGTGAATCGAACGAAATTTCATTCCT 60.073 34.615 18.46 6.25 30.28 3.36
2273 3137 0.257905 TAGGAACCCTCTAGCTCGCA 59.742 55.000 0.00 0.00 34.61 5.10
2291 3158 3.352338 AACCGTTCGCGAGCTAGGG 62.352 63.158 20.77 17.49 44.71 3.53
2303 3170 1.682005 GCTAGGGGTGGCATTTGCA 60.682 57.895 4.74 0.00 44.36 4.08
2309 3176 1.229975 GGGTGGCATTTGCAAACTGC 61.230 55.000 25.55 25.55 45.29 4.40
2311 3178 3.553039 GGCATTTGCAAACTGCCG 58.447 55.556 31.45 15.59 45.35 5.69
2312 3179 2.028733 GGCATTTGCAAACTGCCGG 61.029 57.895 31.45 14.93 45.35 6.13
2315 3182 0.945265 CATTTGCAAACTGCCGGGTG 60.945 55.000 15.41 2.18 44.23 4.61
2321 3188 1.227853 AAACTGCCGGGTGACAGTC 60.228 57.895 12.14 0.00 46.17 3.51
2330 3197 2.224209 CCGGGTGACAGTCTTAGTGTTT 60.224 50.000 1.31 0.00 30.64 2.83
2331 3198 3.463944 CGGGTGACAGTCTTAGTGTTTT 58.536 45.455 1.31 0.00 30.64 2.43
2332 3199 3.875134 CGGGTGACAGTCTTAGTGTTTTT 59.125 43.478 1.31 0.00 30.64 1.94
2333 3200 4.260620 CGGGTGACAGTCTTAGTGTTTTTG 60.261 45.833 1.31 0.00 30.64 2.44
2334 3201 4.036380 GGGTGACAGTCTTAGTGTTTTTGG 59.964 45.833 1.31 0.00 30.64 3.28
2335 3202 4.879545 GGTGACAGTCTTAGTGTTTTTGGA 59.120 41.667 1.31 0.00 30.64 3.53
2336 3203 5.531287 GGTGACAGTCTTAGTGTTTTTGGAT 59.469 40.000 1.31 0.00 30.64 3.41
2337 3204 6.430451 GTGACAGTCTTAGTGTTTTTGGATG 58.570 40.000 1.31 0.00 30.64 3.51
2338 3205 5.530915 TGACAGTCTTAGTGTTTTTGGATGG 59.469 40.000 1.31 0.00 30.64 3.51
2339 3206 4.278419 ACAGTCTTAGTGTTTTTGGATGGC 59.722 41.667 0.00 0.00 0.00 4.40
2340 3207 4.278170 CAGTCTTAGTGTTTTTGGATGGCA 59.722 41.667 0.00 0.00 0.00 4.92
2341 3208 4.892934 AGTCTTAGTGTTTTTGGATGGCAA 59.107 37.500 0.00 0.00 0.00 4.52
2342 3209 5.539955 AGTCTTAGTGTTTTTGGATGGCAAT 59.460 36.000 0.00 0.00 0.00 3.56
2343 3210 6.041979 AGTCTTAGTGTTTTTGGATGGCAATT 59.958 34.615 0.00 0.00 0.00 2.32
2344 3211 6.705825 GTCTTAGTGTTTTTGGATGGCAATTT 59.294 34.615 0.00 0.00 0.00 1.82
2345 3212 7.226523 GTCTTAGTGTTTTTGGATGGCAATTTT 59.773 33.333 0.00 0.00 0.00 1.82
2346 3213 7.772757 TCTTAGTGTTTTTGGATGGCAATTTTT 59.227 29.630 0.00 0.00 0.00 1.94
2347 3214 6.134040 AGTGTTTTTGGATGGCAATTTTTG 57.866 33.333 0.00 0.00 0.00 2.44
2361 3228 3.629438 ATTTTTGCACAAAAGCATGGC 57.371 38.095 1.52 0.00 45.19 4.40
2362 3229 2.034104 TTTTGCACAAAAGCATGGCA 57.966 40.000 4.47 0.00 45.19 4.92
2363 3230 2.257691 TTTGCACAAAAGCATGGCAT 57.742 40.000 0.00 0.00 45.19 4.40
2364 3231 2.257691 TTGCACAAAAGCATGGCATT 57.742 40.000 0.00 0.00 45.19 3.56
2365 3232 2.257691 TGCACAAAAGCATGGCATTT 57.742 40.000 0.00 0.00 40.11 2.32
2366 3233 2.573369 TGCACAAAAGCATGGCATTTT 58.427 38.095 0.00 0.00 40.11 1.82
2367 3234 2.290916 TGCACAAAAGCATGGCATTTTG 59.709 40.909 18.41 18.41 46.77 2.44
2378 3245 4.858140 GCATGGCATTTTGTTTATTTTGGC 59.142 37.500 0.00 0.00 0.00 4.52
2381 3248 3.058639 GGCATTTTGTTTATTTTGGCGCA 60.059 39.130 10.83 0.00 0.00 6.09
2388 3255 4.433615 TGTTTATTTTGGCGCAGTTTTCA 58.566 34.783 10.83 0.00 0.00 2.69
2393 3260 0.597568 TTGGCGCAGTTTTCATCCAG 59.402 50.000 10.83 0.00 0.00 3.86
2409 3276 0.817634 CCAGAAACTGCCACCGTCAA 60.818 55.000 0.00 0.00 0.00 3.18
2415 3282 2.851263 ACTGCCACCGTCAAATCTTA 57.149 45.000 0.00 0.00 0.00 2.10
2423 3290 5.153513 CCACCGTCAAATCTTAATTGTGTG 58.846 41.667 0.00 0.00 0.00 3.82
2425 3292 4.165779 CCGTCAAATCTTAATTGTGTGGC 58.834 43.478 0.00 0.00 0.00 5.01
2428 3295 4.851558 GTCAAATCTTAATTGTGTGGCGTC 59.148 41.667 0.00 0.00 0.00 5.19
2432 3299 1.468520 CTTAATTGTGTGGCGTCTGGG 59.531 52.381 0.00 0.00 0.00 4.45
2434 3301 0.889186 AATTGTGTGGCGTCTGGGAC 60.889 55.000 0.00 0.00 0.00 4.46
2454 3333 2.224018 ACGTTGTTCCTAGCAACCGTTA 60.224 45.455 0.00 0.00 42.12 3.18
2457 3336 3.308438 TGTTCCTAGCAACCGTTAGTC 57.692 47.619 0.00 0.00 0.00 2.59
2460 3339 1.822990 TCCTAGCAACCGTTAGTCAGG 59.177 52.381 0.00 0.00 0.00 3.86
2468 3347 4.378046 GCAACCGTTAGTCAGGTAACATTG 60.378 45.833 0.00 0.00 40.37 2.82
2482 3361 8.524487 TCAGGTAACATTGCCGTAAAATTATTT 58.476 29.630 0.00 0.00 38.06 1.40
2503 3382 7.914427 ATTTGACCTTTAAAAAGAAGACCCT 57.086 32.000 4.01 0.00 38.28 4.34
2513 3392 8.747538 TTAAAAAGAAGACCCTAATATCTGGC 57.252 34.615 0.00 0.00 0.00 4.85
2518 3397 3.928754 AGACCCTAATATCTGGCTGACA 58.071 45.455 0.00 0.00 0.00 3.58
2531 3410 0.818445 GCTGACAGATGCCATGGGAG 60.818 60.000 15.13 1.04 0.00 4.30
2547 3426 1.080705 GAGGTGGTCCTGACGAACG 60.081 63.158 0.00 0.00 45.24 3.95
2549 3428 0.898789 AGGTGGTCCTGACGAACGAT 60.899 55.000 0.14 0.00 43.33 3.73
2550 3429 0.037605 GGTGGTCCTGACGAACGATT 60.038 55.000 0.14 0.00 0.00 3.34
2551 3430 1.347320 GTGGTCCTGACGAACGATTC 58.653 55.000 0.14 0.00 0.00 2.52
2552 3431 0.963225 TGGTCCTGACGAACGATTCA 59.037 50.000 0.14 0.00 0.00 2.57
2553 3432 1.548719 TGGTCCTGACGAACGATTCAT 59.451 47.619 0.14 0.00 0.00 2.57
2554 3433 2.028476 TGGTCCTGACGAACGATTCATT 60.028 45.455 0.14 0.00 0.00 2.57
2555 3434 3.000727 GGTCCTGACGAACGATTCATTT 58.999 45.455 0.14 0.00 0.00 2.32
2556 3435 3.181520 GGTCCTGACGAACGATTCATTTG 60.182 47.826 0.14 0.00 0.00 2.32
2557 3436 2.415168 TCCTGACGAACGATTCATTTGC 59.585 45.455 0.14 0.00 0.00 3.68
2558 3437 2.476185 CCTGACGAACGATTCATTTGCC 60.476 50.000 0.14 0.00 0.00 4.52
2559 3438 1.466950 TGACGAACGATTCATTTGCCC 59.533 47.619 0.14 0.00 0.00 5.36
2560 3439 1.737793 GACGAACGATTCATTTGCCCT 59.262 47.619 0.14 0.00 0.00 5.19
2561 3440 1.468520 ACGAACGATTCATTTGCCCTG 59.531 47.619 0.14 0.00 0.00 4.45
2562 3441 1.795162 CGAACGATTCATTTGCCCTGC 60.795 52.381 0.00 0.00 0.00 4.85
2563 3442 1.202114 GAACGATTCATTTGCCCTGCA 59.798 47.619 0.00 0.00 36.47 4.41
2575 3454 4.888326 TTGCCCTGCAAACTAAATCATT 57.112 36.364 0.00 0.00 45.96 2.57
2576 3455 4.454728 TGCCCTGCAAACTAAATCATTC 57.545 40.909 0.00 0.00 34.76 2.67
2577 3456 3.119531 TGCCCTGCAAACTAAATCATTCG 60.120 43.478 0.00 0.00 34.76 3.34
2578 3457 3.438360 CCCTGCAAACTAAATCATTCGC 58.562 45.455 0.00 0.00 0.00 4.70
2579 3458 3.129287 CCCTGCAAACTAAATCATTCGCT 59.871 43.478 0.00 0.00 0.00 4.93
2580 3459 4.100529 CCTGCAAACTAAATCATTCGCTG 58.899 43.478 0.00 0.00 0.00 5.18
2581 3460 4.095410 TGCAAACTAAATCATTCGCTGG 57.905 40.909 0.00 0.00 0.00 4.85
2582 3461 3.119531 TGCAAACTAAATCATTCGCTGGG 60.120 43.478 0.00 0.00 0.00 4.45
2583 3462 3.734902 GCAAACTAAATCATTCGCTGGGG 60.735 47.826 0.00 0.00 0.00 4.96
2584 3463 1.680338 ACTAAATCATTCGCTGGGGC 58.320 50.000 0.00 0.00 0.00 5.80
2585 3464 1.064758 ACTAAATCATTCGCTGGGGCA 60.065 47.619 0.00 0.00 38.60 5.36
2586 3465 2.023673 CTAAATCATTCGCTGGGGCAA 58.976 47.619 0.00 0.00 38.60 4.52
2587 3466 1.265236 AAATCATTCGCTGGGGCAAA 58.735 45.000 0.00 0.00 38.60 3.68
2588 3467 1.265236 AATCATTCGCTGGGGCAAAA 58.735 45.000 0.00 0.00 38.60 2.44
2589 3468 1.265236 ATCATTCGCTGGGGCAAAAA 58.735 45.000 0.00 0.00 38.60 1.94
2617 3496 1.192803 ACAACGAACCCCTCCCTCTC 61.193 60.000 0.00 0.00 0.00 3.20
2627 3506 1.688311 CCCTCCCTCTCCACGACAATA 60.688 57.143 0.00 0.00 0.00 1.90
2628 3507 1.683917 CCTCCCTCTCCACGACAATAG 59.316 57.143 0.00 0.00 0.00 1.73
2629 3508 2.379972 CTCCCTCTCCACGACAATAGT 58.620 52.381 0.00 0.00 0.00 2.12
2636 3515 5.105877 CCTCTCCACGACAATAGTTAAGACA 60.106 44.000 0.00 0.00 0.00 3.41
2637 3516 6.405953 CCTCTCCACGACAATAGTTAAGACAT 60.406 42.308 0.00 0.00 0.00 3.06
2638 3517 6.561614 TCTCCACGACAATAGTTAAGACATC 58.438 40.000 0.00 0.00 0.00 3.06
2649 3528 1.367346 TAAGACATCCAGTTGGGCCA 58.633 50.000 0.00 0.00 36.21 5.36
2650 3529 0.482446 AAGACATCCAGTTGGGCCAA 59.518 50.000 16.66 16.66 36.21 4.52
2651 3530 0.482446 AGACATCCAGTTGGGCCAAA 59.518 50.000 22.82 5.53 36.21 3.28
2674 3553 4.776795 AAAAACGTTTTCCTGACACACT 57.223 36.364 25.37 4.20 0.00 3.55
2683 3562 6.036300 CGTTTTCCTGACACACTACAAAACTA 59.964 38.462 0.00 0.00 0.00 2.24
2709 3588 5.904362 AATTGCTACTTGGACCTCATTTC 57.096 39.130 0.00 0.00 0.00 2.17
2714 3593 5.183713 TGCTACTTGGACCTCATTTCAAATG 59.816 40.000 3.46 3.46 0.00 2.32
2758 3637 8.915871 AAAATACATAGCAGCATACTGTTTTG 57.084 30.769 0.00 0.00 46.30 2.44
2759 3638 7.864108 AATACATAGCAGCATACTGTTTTGA 57.136 32.000 7.13 0.00 46.30 2.69
2760 3639 8.455903 AATACATAGCAGCATACTGTTTTGAT 57.544 30.769 7.13 0.00 46.30 2.57
2761 3640 9.559732 AATACATAGCAGCATACTGTTTTGATA 57.440 29.630 7.13 0.00 46.30 2.15
2762 3641 7.488187 ACATAGCAGCATACTGTTTTGATAG 57.512 36.000 7.13 0.00 46.30 2.08
2763 3642 7.275183 ACATAGCAGCATACTGTTTTGATAGA 58.725 34.615 7.13 0.00 46.30 1.98
2764 3643 7.770433 ACATAGCAGCATACTGTTTTGATAGAA 59.230 33.333 7.13 0.00 46.30 2.10
2765 3644 8.615211 CATAGCAGCATACTGTTTTGATAGAAA 58.385 33.333 0.00 0.00 46.30 2.52
2776 3655 6.990798 TGTTTTGATAGAAATGCCATGACAA 58.009 32.000 0.00 0.00 0.00 3.18
2778 3657 7.384660 TGTTTTGATAGAAATGCCATGACAAAC 59.615 33.333 0.00 0.00 0.00 2.93
2781 3660 1.612950 AGAAATGCCATGACAAACGCA 59.387 42.857 0.00 0.00 35.35 5.24
2784 3663 2.522836 ATGCCATGACAAACGCAAAA 57.477 40.000 0.00 0.00 34.38 2.44
2787 3666 2.543012 TGCCATGACAAACGCAAAATTG 59.457 40.909 0.00 0.00 0.00 2.32
2805 3684 8.816144 GCAAAATTGTTTGAAAACTCTCATACA 58.184 29.630 7.39 0.00 45.99 2.29
2812 3691 9.567848 TGTTTGAAAACTCTCATACAGAAAAAC 57.432 29.630 7.39 0.00 39.59 2.43
2822 3706 9.261180 CTCTCATACAGAAAAACTTAGAACACA 57.739 33.333 0.00 0.00 0.00 3.72
2825 3709 9.554395 TCATACAGAAAAACTTAGAACACATGA 57.446 29.630 0.00 0.00 0.00 3.07
2839 3723 9.689976 TTAGAACACATGAAATTTACAACATGG 57.310 29.630 17.21 10.94 42.66 3.66
2845 3729 4.252073 TGAAATTTACAACATGGCATGCC 58.748 39.130 30.54 30.54 0.00 4.40
2846 3730 2.985957 ATTTACAACATGGCATGCCC 57.014 45.000 33.44 16.23 34.56 5.36
2860 3746 5.396485 TGGCATGCCCTAGATGATAAAAAT 58.604 37.500 33.44 0.00 34.56 1.82
2862 3748 6.161381 GGCATGCCCTAGATGATAAAAATTG 58.839 40.000 27.24 0.00 0.00 2.32
2863 3749 6.161381 GCATGCCCTAGATGATAAAAATTGG 58.839 40.000 6.36 0.00 0.00 3.16
2868 3754 6.161381 CCCTAGATGATAAAAATTGGCATGC 58.839 40.000 9.90 9.90 0.00 4.06
2910 3796 2.460757 AATTGGCATGGCTGTGAAAC 57.539 45.000 21.08 0.00 37.35 2.78
2931 3817 5.599999 ACAGACATACCAGTGGAATAGAC 57.400 43.478 18.40 3.30 0.00 2.59
2936 3822 6.495181 AGACATACCAGTGGAATAGACATAGG 59.505 42.308 18.40 0.00 0.00 2.57
2937 3823 6.382087 ACATACCAGTGGAATAGACATAGGA 58.618 40.000 18.40 0.00 0.00 2.94
2942 3828 6.012858 ACCAGTGGAATAGACATAGGAAACAA 60.013 38.462 18.40 0.00 0.00 2.83
2980 3869 3.234353 TGACATGCTAGCTACTATGGCT 58.766 45.455 17.23 0.00 43.02 4.75
2981 3870 4.407365 TGACATGCTAGCTACTATGGCTA 58.593 43.478 17.23 1.98 40.74 3.93
2990 3879 5.913137 AGCTACTATGGCTATGCTCTAAG 57.087 43.478 0.00 0.00 38.36 2.18
2996 3885 6.696411 ACTATGGCTATGCTCTAAGAACATC 58.304 40.000 0.00 0.00 0.00 3.06
3000 3889 7.308450 TGGCTATGCTCTAAGAACATCTAAT 57.692 36.000 0.00 0.00 0.00 1.73
3046 3935 8.732854 AGGAATAGACATAAAATTACCATGGGA 58.267 33.333 18.09 3.85 0.00 4.37
3054 3943 5.835113 AAAATTACCATGGGAAGATGTCG 57.165 39.130 16.30 0.00 0.00 4.35
3057 3946 4.561500 TTACCATGGGAAGATGTCGAAA 57.438 40.909 18.09 0.00 0.00 3.46
3058 3947 3.433306 ACCATGGGAAGATGTCGAAAA 57.567 42.857 18.09 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.961019 TGCCAGTCATTGCAAGGTTC 59.039 50.000 11.36 6.02 33.87 3.62
10 11 1.304630 TGCCATTGCTGCCAGTCAT 60.305 52.632 0.00 0.00 38.71 3.06
11 12 1.974875 CTGCCATTGCTGCCAGTCA 60.975 57.895 0.00 0.00 38.71 3.41
30 31 8.416329 GCTCAACCTTTATTATCACCAATGATT 58.584 33.333 0.00 0.00 43.40 2.57
34 35 7.961326 AAGCTCAACCTTTATTATCACCAAT 57.039 32.000 0.00 0.00 0.00 3.16
62 63 1.034356 AACACACATGCACAGCACAT 58.966 45.000 0.00 0.00 43.04 3.21
73 74 4.318332 CTCACTCCACACATAACACACAT 58.682 43.478 0.00 0.00 0.00 3.21
81 82 1.202348 CACTCGCTCACTCCACACATA 59.798 52.381 0.00 0.00 0.00 2.29
97 98 4.392138 GCCAAATCACCAACTACTACACTC 59.608 45.833 0.00 0.00 0.00 3.51
170 171 0.741221 GACAATCGCTCCCTCACCAC 60.741 60.000 0.00 0.00 0.00 4.16
224 226 3.357079 CACCAGACGCTGCAACCC 61.357 66.667 0.00 0.00 0.00 4.11
319 321 0.107831 GAACACACCACTACCCAGCA 59.892 55.000 0.00 0.00 0.00 4.41
352 354 1.675641 CCGCCCCTCCACAAAGAAG 60.676 63.158 0.00 0.00 0.00 2.85
357 359 2.196997 CTCAATCCGCCCCTCCACAA 62.197 60.000 0.00 0.00 0.00 3.33
358 360 2.609299 TCAATCCGCCCCTCCACA 60.609 61.111 0.00 0.00 0.00 4.17
364 366 2.825836 CTGCACTCAATCCGCCCC 60.826 66.667 0.00 0.00 0.00 5.80
378 380 2.817423 CGAGGCGAAATGGAGCTGC 61.817 63.158 0.00 0.00 0.00 5.25
404 406 5.001874 GGACAAAACGGAAGAGAATTACCT 58.998 41.667 0.00 0.00 0.00 3.08
419 421 1.335872 CGGGCATTCACAGGACAAAAC 60.336 52.381 0.00 0.00 0.00 2.43
423 425 2.359850 GCGGGCATTCACAGGACA 60.360 61.111 0.00 0.00 0.00 4.02
446 448 1.159285 CACGGTCTGCACATGAACAT 58.841 50.000 0.00 0.00 0.00 2.71
454 456 1.359848 CAACTATCCACGGTCTGCAC 58.640 55.000 0.00 0.00 0.00 4.57
463 465 0.702316 AACCCCACCCAACTATCCAC 59.298 55.000 0.00 0.00 0.00 4.02
468 470 1.357272 ACTGCAACCCCACCCAACTA 61.357 55.000 0.00 0.00 0.00 2.24
473 475 1.152546 AAGAACTGCAACCCCACCC 60.153 57.895 0.00 0.00 0.00 4.61
476 478 0.843309 TCTGAAGAACTGCAACCCCA 59.157 50.000 0.00 0.00 0.00 4.96
477 479 2.206576 ATCTGAAGAACTGCAACCCC 57.793 50.000 0.00 0.00 0.00 4.95
478 480 3.149196 TGAATCTGAAGAACTGCAACCC 58.851 45.455 0.00 0.00 0.00 4.11
479 481 4.436584 CGATGAATCTGAAGAACTGCAACC 60.437 45.833 0.00 0.00 0.00 3.77
480 482 4.436584 CCGATGAATCTGAAGAACTGCAAC 60.437 45.833 0.00 0.00 0.00 4.17
482 484 3.055891 TCCGATGAATCTGAAGAACTGCA 60.056 43.478 0.00 0.00 0.00 4.41
483 485 3.525537 TCCGATGAATCTGAAGAACTGC 58.474 45.455 0.00 0.00 0.00 4.40
484 486 4.025061 GCATCCGATGAATCTGAAGAACTG 60.025 45.833 12.79 0.00 0.00 3.16
485 487 4.125703 GCATCCGATGAATCTGAAGAACT 58.874 43.478 12.79 0.00 0.00 3.01
487 489 3.126073 CGCATCCGATGAATCTGAAGAA 58.874 45.455 12.79 0.00 36.29 2.52
666 710 5.059343 CGAGAATATATAAACCACAGACGCG 59.941 44.000 3.53 3.53 0.00 6.01
701 747 4.287067 GGCACTCTCCCCTAATGATCATTA 59.713 45.833 23.46 23.46 32.50 1.90
709 755 0.988678 GGTGGGCACTCTCCCCTAAT 60.989 60.000 0.00 0.00 45.97 1.73
726 775 6.825610 TGGCACTTTTAAATGAAATTCAGGT 58.174 32.000 8.00 0.00 33.67 4.00
809 860 6.639632 AAACTACTCCGTGTAAGTAACTGA 57.360 37.500 0.00 0.00 0.00 3.41
810 861 7.536622 CACTAAACTACTCCGTGTAAGTAACTG 59.463 40.741 0.00 0.00 0.00 3.16
811 862 7.229506 ACACTAAACTACTCCGTGTAAGTAACT 59.770 37.037 0.00 0.00 37.09 2.24
812 863 7.363431 ACACTAAACTACTCCGTGTAAGTAAC 58.637 38.462 0.00 0.00 37.09 2.50
813 864 7.510549 ACACTAAACTACTCCGTGTAAGTAA 57.489 36.000 0.00 0.00 37.09 2.24
814 865 6.128553 CGACACTAAACTACTCCGTGTAAGTA 60.129 42.308 0.00 0.00 38.77 2.24
866 917 4.220382 CCACAAATCTCTATGCCAAAACCA 59.780 41.667 0.00 0.00 0.00 3.67
873 924 1.953559 TCGCCACAAATCTCTATGCC 58.046 50.000 0.00 0.00 0.00 4.40
959 1010 5.354767 TCGCATCCTATACGATACGATACT 58.645 41.667 3.72 0.00 34.04 2.12
1080 1140 2.035832 CCACAACAGTTTGGATTGGGAC 59.964 50.000 8.17 0.00 37.00 4.46
2065 2432 2.124507 TAGAAACAAGGCAGCCCGCT 62.125 55.000 8.22 0.00 41.91 5.52
2068 2435 0.881796 GTGTAGAAACAAGGCAGCCC 59.118 55.000 8.22 0.00 37.36 5.19
2075 2442 3.063997 GGCGATCCATGTGTAGAAACAAG 59.936 47.826 0.00 0.00 37.36 3.16
2076 2443 3.006940 GGCGATCCATGTGTAGAAACAA 58.993 45.455 0.00 0.00 37.36 2.83
2077 2444 2.027653 TGGCGATCCATGTGTAGAAACA 60.028 45.455 0.00 0.00 37.47 2.83
2078 2445 2.627945 TGGCGATCCATGTGTAGAAAC 58.372 47.619 0.00 0.00 37.47 2.78
2089 2456 3.369052 ACGAAGTTAAGAATGGCGATCCA 60.369 43.478 0.00 0.00 43.77 3.41
2090 2457 3.195661 ACGAAGTTAAGAATGGCGATCC 58.804 45.455 0.00 0.00 37.78 3.36
2161 2528 4.023963 GGCTTGGTTTTCTGTTACAGAGAC 60.024 45.833 14.99 16.24 41.75 3.36
2163 2530 3.882888 TGGCTTGGTTTTCTGTTACAGAG 59.117 43.478 14.99 3.40 41.75 3.35
2209 2578 5.403466 CCTTCTCGCAAAAAGAAAAGGAATG 59.597 40.000 0.00 0.00 32.60 2.67
2210 2579 5.532557 CCTTCTCGCAAAAAGAAAAGGAAT 58.467 37.500 0.00 0.00 32.60 3.01
2211 2580 4.736464 GCCTTCTCGCAAAAAGAAAAGGAA 60.736 41.667 2.80 0.00 32.60 3.36
2213 2582 3.052745 GCCTTCTCGCAAAAAGAAAAGG 58.947 45.455 0.00 0.00 32.60 3.11
2215 2584 2.428890 TGGCCTTCTCGCAAAAAGAAAA 59.571 40.909 3.32 0.00 32.60 2.29
2273 3137 2.181021 CCTAGCTCGCGAACGGTT 59.819 61.111 11.33 0.00 40.63 4.44
2286 3153 1.066929 GTTTGCAAATGCCACCCCTAG 60.067 52.381 16.21 0.00 41.18 3.02
2291 3158 2.237416 GCAGTTTGCAAATGCCACC 58.763 52.632 24.23 10.12 44.26 4.61
2303 3170 1.227853 GACTGTCACCCGGCAGTTT 60.228 57.895 12.87 0.00 44.89 2.66
2309 3176 0.966920 ACACTAAGACTGTCACCCGG 59.033 55.000 10.88 0.00 0.00 5.73
2310 3177 2.814280 AACACTAAGACTGTCACCCG 57.186 50.000 10.88 0.00 0.00 5.28
2311 3178 4.036380 CCAAAAACACTAAGACTGTCACCC 59.964 45.833 10.88 0.00 0.00 4.61
2312 3179 4.879545 TCCAAAAACACTAAGACTGTCACC 59.120 41.667 10.88 0.00 0.00 4.02
2315 3182 5.562890 GCCATCCAAAAACACTAAGACTGTC 60.563 44.000 0.00 0.00 0.00 3.51
2321 3188 7.495135 AAAATTGCCATCCAAAAACACTAAG 57.505 32.000 0.00 0.00 36.92 2.18
2339 3206 3.731717 GCCATGCTTTTGTGCAAAAATTG 59.268 39.130 2.11 0.92 46.61 2.32
2340 3207 3.380637 TGCCATGCTTTTGTGCAAAAATT 59.619 34.783 2.11 0.00 46.61 1.82
2341 3208 2.950309 TGCCATGCTTTTGTGCAAAAAT 59.050 36.364 2.11 1.31 46.61 1.82
2342 3209 2.362736 TGCCATGCTTTTGTGCAAAAA 58.637 38.095 10.70 0.00 46.61 1.94
2343 3210 2.034104 TGCCATGCTTTTGTGCAAAA 57.966 40.000 9.37 9.37 46.61 2.44
2344 3211 2.257691 ATGCCATGCTTTTGTGCAAA 57.742 40.000 0.00 0.00 46.61 3.68
2345 3212 2.257691 AATGCCATGCTTTTGTGCAA 57.742 40.000 0.00 0.00 46.61 4.08
2347 3214 2.923643 CAAAATGCCATGCTTTTGTGC 58.076 42.857 13.77 1.01 37.50 4.57
2350 3217 8.480853 CAAAATAAACAAAATGCCATGCTTTTG 58.519 29.630 17.63 17.63 44.22 2.44
2351 3218 7.652507 CCAAAATAAACAAAATGCCATGCTTTT 59.347 29.630 0.00 0.00 37.47 2.27
2352 3219 7.146648 CCAAAATAAACAAAATGCCATGCTTT 58.853 30.769 0.00 0.00 0.00 3.51
2353 3220 6.679843 CCAAAATAAACAAAATGCCATGCTT 58.320 32.000 0.00 0.00 0.00 3.91
2354 3221 5.335819 GCCAAAATAAACAAAATGCCATGCT 60.336 36.000 0.00 0.00 0.00 3.79
2355 3222 4.858140 GCCAAAATAAACAAAATGCCATGC 59.142 37.500 0.00 0.00 0.00 4.06
2356 3223 5.087397 CGCCAAAATAAACAAAATGCCATG 58.913 37.500 0.00 0.00 0.00 3.66
2357 3224 4.379290 GCGCCAAAATAAACAAAATGCCAT 60.379 37.500 0.00 0.00 0.00 4.40
2358 3225 3.058639 GCGCCAAAATAAACAAAATGCCA 60.059 39.130 0.00 0.00 0.00 4.92
2359 3226 3.058639 TGCGCCAAAATAAACAAAATGCC 60.059 39.130 4.18 0.00 0.00 4.40
2360 3227 4.139183 TGCGCCAAAATAAACAAAATGC 57.861 36.364 4.18 0.00 0.00 3.56
2361 3228 5.341407 ACTGCGCCAAAATAAACAAAATG 57.659 34.783 4.18 0.00 0.00 2.32
2362 3229 6.370433 AAACTGCGCCAAAATAAACAAAAT 57.630 29.167 4.18 0.00 0.00 1.82
2363 3230 5.803020 AAACTGCGCCAAAATAAACAAAA 57.197 30.435 4.18 0.00 0.00 2.44
2364 3231 5.351465 TGAAAACTGCGCCAAAATAAACAAA 59.649 32.000 4.18 0.00 0.00 2.83
2365 3232 4.870426 TGAAAACTGCGCCAAAATAAACAA 59.130 33.333 4.18 0.00 0.00 2.83
2366 3233 4.433615 TGAAAACTGCGCCAAAATAAACA 58.566 34.783 4.18 0.00 0.00 2.83
2367 3234 5.389411 GGATGAAAACTGCGCCAAAATAAAC 60.389 40.000 4.18 0.00 0.00 2.01
2368 3235 4.688413 GGATGAAAACTGCGCCAAAATAAA 59.312 37.500 4.18 0.00 0.00 1.40
2378 3245 3.558505 CAGTTTCTGGATGAAAACTGCG 58.441 45.455 13.19 0.00 45.10 5.18
2381 3248 3.319122 GTGGCAGTTTCTGGATGAAAACT 59.681 43.478 0.00 0.00 45.10 2.66
2388 3255 0.321653 GACGGTGGCAGTTTCTGGAT 60.322 55.000 0.00 0.00 31.21 3.41
2393 3260 1.880027 AGATTTGACGGTGGCAGTTTC 59.120 47.619 0.00 0.00 0.00 2.78
2409 3276 3.440173 CCAGACGCCACACAATTAAGATT 59.560 43.478 0.00 0.00 0.00 2.40
2415 3282 0.889186 GTCCCAGACGCCACACAATT 60.889 55.000 0.00 0.00 0.00 2.32
2428 3295 0.320374 TGCTAGGAACAACGTCCCAG 59.680 55.000 0.00 0.00 38.59 4.45
2432 3299 0.788391 CGGTTGCTAGGAACAACGTC 59.212 55.000 25.90 9.39 46.65 4.34
2434 3301 1.223187 AACGGTTGCTAGGAACAACG 58.777 50.000 25.90 22.16 46.65 4.10
2454 3333 3.688694 TTACGGCAATGTTACCTGACT 57.311 42.857 0.00 0.00 0.00 3.41
2457 3336 8.591312 CAAATAATTTTACGGCAATGTTACCTG 58.409 33.333 0.00 0.00 0.00 4.00
2460 3339 8.588789 GGTCAAATAATTTTACGGCAATGTTAC 58.411 33.333 0.00 0.00 0.00 2.50
2494 3373 4.591072 GTCAGCCAGATATTAGGGTCTTCT 59.409 45.833 0.00 0.00 32.31 2.85
2495 3374 4.345257 TGTCAGCCAGATATTAGGGTCTTC 59.655 45.833 0.00 0.00 32.31 2.87
2497 3376 3.900601 CTGTCAGCCAGATATTAGGGTCT 59.099 47.826 0.00 0.00 44.49 3.85
2498 3377 3.898123 TCTGTCAGCCAGATATTAGGGTC 59.102 47.826 0.00 0.00 45.34 4.46
2499 3378 3.928754 TCTGTCAGCCAGATATTAGGGT 58.071 45.455 0.00 0.00 45.34 4.34
2513 3392 0.179026 CCTCCCATGGCATCTGTCAG 60.179 60.000 6.09 0.00 30.80 3.51
2518 3397 1.620589 ACCACCTCCCATGGCATCT 60.621 57.895 6.09 0.00 41.31 2.90
2519 3398 1.152881 GACCACCTCCCATGGCATC 60.153 63.158 6.09 0.00 41.31 3.91
2521 3400 3.338250 GGACCACCTCCCATGGCA 61.338 66.667 6.09 0.00 41.31 4.92
2526 3405 2.603473 CGTCAGGACCACCTCCCA 60.603 66.667 0.00 0.00 45.94 4.37
2531 3410 0.037605 AATCGTTCGTCAGGACCACC 60.038 55.000 0.00 0.00 0.00 4.61
2555 3434 3.119531 CGAATGATTTAGTTTGCAGGGCA 60.120 43.478 0.00 0.00 36.47 5.36
2556 3435 3.438360 CGAATGATTTAGTTTGCAGGGC 58.562 45.455 0.00 0.00 0.00 5.19
2557 3436 3.129287 AGCGAATGATTTAGTTTGCAGGG 59.871 43.478 0.00 0.00 37.23 4.45
2558 3437 4.100529 CAGCGAATGATTTAGTTTGCAGG 58.899 43.478 0.00 0.00 37.23 4.85
2559 3438 4.100529 CCAGCGAATGATTTAGTTTGCAG 58.899 43.478 0.00 0.00 37.23 4.41
2560 3439 3.119531 CCCAGCGAATGATTTAGTTTGCA 60.120 43.478 0.00 0.00 37.23 4.08
2561 3440 3.438360 CCCAGCGAATGATTTAGTTTGC 58.562 45.455 0.00 0.00 35.43 3.68
2562 3441 3.734902 GCCCCAGCGAATGATTTAGTTTG 60.735 47.826 0.00 0.00 0.00 2.93
2563 3442 2.427095 GCCCCAGCGAATGATTTAGTTT 59.573 45.455 0.00 0.00 0.00 2.66
2564 3443 2.024414 GCCCCAGCGAATGATTTAGTT 58.976 47.619 0.00 0.00 0.00 2.24
2565 3444 1.064758 TGCCCCAGCGAATGATTTAGT 60.065 47.619 0.00 0.00 44.31 2.24
2566 3445 1.679139 TGCCCCAGCGAATGATTTAG 58.321 50.000 0.00 0.00 44.31 1.85
2567 3446 2.136298 TTGCCCCAGCGAATGATTTA 57.864 45.000 0.00 0.00 44.31 1.40
2568 3447 1.265236 TTTGCCCCAGCGAATGATTT 58.735 45.000 0.00 0.00 44.31 2.17
2569 3448 1.265236 TTTTGCCCCAGCGAATGATT 58.735 45.000 0.00 0.00 42.09 2.57
2570 3449 1.265236 TTTTTGCCCCAGCGAATGAT 58.735 45.000 0.00 0.00 42.09 2.45
2571 3450 2.738812 TTTTTGCCCCAGCGAATGA 58.261 47.368 0.00 0.00 42.09 2.57
2594 3473 1.063492 AGGGAGGGGTTCGTTGTTTTT 60.063 47.619 0.00 0.00 0.00 1.94
2595 3474 0.554305 AGGGAGGGGTTCGTTGTTTT 59.446 50.000 0.00 0.00 0.00 2.43
2596 3475 0.109913 GAGGGAGGGGTTCGTTGTTT 59.890 55.000 0.00 0.00 0.00 2.83
2597 3476 0.767060 AGAGGGAGGGGTTCGTTGTT 60.767 55.000 0.00 0.00 0.00 2.83
2598 3477 1.152096 AGAGGGAGGGGTTCGTTGT 60.152 57.895 0.00 0.00 0.00 3.32
2599 3478 1.597461 GAGAGGGAGGGGTTCGTTG 59.403 63.158 0.00 0.00 0.00 4.10
2600 3479 1.612739 GGAGAGGGAGGGGTTCGTT 60.613 63.158 0.00 0.00 0.00 3.85
2601 3480 2.039137 GGAGAGGGAGGGGTTCGT 59.961 66.667 0.00 0.00 0.00 3.85
2602 3481 2.038975 TGGAGAGGGAGGGGTTCG 59.961 66.667 0.00 0.00 0.00 3.95
2603 3482 2.359967 CGTGGAGAGGGAGGGGTTC 61.360 68.421 0.00 0.00 0.00 3.62
2617 3496 5.416083 TGGATGTCTTAACTATTGTCGTGG 58.584 41.667 0.00 0.00 0.00 4.94
2627 3506 2.290960 GGCCCAACTGGATGTCTTAACT 60.291 50.000 0.00 0.00 37.39 2.24
2628 3507 2.092323 GGCCCAACTGGATGTCTTAAC 58.908 52.381 0.00 0.00 37.39 2.01
2629 3508 1.707989 TGGCCCAACTGGATGTCTTAA 59.292 47.619 0.00 0.00 37.39 1.85
2659 3538 6.190954 AGTTTTGTAGTGTGTCAGGAAAAC 57.809 37.500 0.00 0.00 33.85 2.43
2689 3568 4.365514 TGAAATGAGGTCCAAGTAGCAA 57.634 40.909 0.00 0.00 0.00 3.91
2697 3576 3.173953 AGCCATTTGAAATGAGGTCCA 57.826 42.857 18.82 0.00 0.00 4.02
2745 3624 6.377996 TGGCATTTCTATCAAAACAGTATGCT 59.622 34.615 0.00 0.00 42.53 3.79
2747 3626 8.407832 TCATGGCATTTCTATCAAAACAGTATG 58.592 33.333 0.00 0.00 46.00 2.39
2748 3627 8.408601 GTCATGGCATTTCTATCAAAACAGTAT 58.591 33.333 0.00 0.00 0.00 2.12
2749 3628 7.392953 TGTCATGGCATTTCTATCAAAACAGTA 59.607 33.333 0.00 0.00 0.00 2.74
2750 3629 6.209192 TGTCATGGCATTTCTATCAAAACAGT 59.791 34.615 0.00 0.00 0.00 3.55
2751 3630 6.623486 TGTCATGGCATTTCTATCAAAACAG 58.377 36.000 0.00 0.00 0.00 3.16
2752 3631 6.587206 TGTCATGGCATTTCTATCAAAACA 57.413 33.333 0.00 0.00 0.00 2.83
2753 3632 7.410728 CGTTTGTCATGGCATTTCTATCAAAAC 60.411 37.037 0.00 0.00 0.00 2.43
2754 3633 6.585702 CGTTTGTCATGGCATTTCTATCAAAA 59.414 34.615 0.00 0.00 0.00 2.44
2755 3634 6.092092 CGTTTGTCATGGCATTTCTATCAAA 58.908 36.000 0.00 1.39 0.00 2.69
2756 3635 5.639757 CGTTTGTCATGGCATTTCTATCAA 58.360 37.500 0.00 0.00 0.00 2.57
2757 3636 4.438608 GCGTTTGTCATGGCATTTCTATCA 60.439 41.667 0.00 0.00 0.00 2.15
2758 3637 4.037690 GCGTTTGTCATGGCATTTCTATC 58.962 43.478 0.00 0.00 0.00 2.08
2759 3638 3.443329 TGCGTTTGTCATGGCATTTCTAT 59.557 39.130 0.00 0.00 0.00 1.98
2760 3639 2.816672 TGCGTTTGTCATGGCATTTCTA 59.183 40.909 0.00 0.00 0.00 2.10
2761 3640 1.612950 TGCGTTTGTCATGGCATTTCT 59.387 42.857 0.00 0.00 0.00 2.52
2762 3641 2.063156 TGCGTTTGTCATGGCATTTC 57.937 45.000 0.00 0.00 0.00 2.17
2763 3642 2.522836 TTGCGTTTGTCATGGCATTT 57.477 40.000 0.00 0.00 35.03 2.32
2764 3643 2.522836 TTTGCGTTTGTCATGGCATT 57.477 40.000 0.00 0.00 35.03 3.56
2765 3644 2.522836 TTTTGCGTTTGTCATGGCAT 57.477 40.000 0.00 0.00 35.03 4.40
2776 3655 6.367422 TGAGAGTTTTCAAACAATTTTGCGTT 59.633 30.769 5.26 0.00 41.78 4.84
2778 3657 6.329838 TGAGAGTTTTCAAACAATTTTGCG 57.670 33.333 5.26 0.00 41.78 4.85
2787 3666 9.788960 AGTTTTTCTGTATGAGAGTTTTCAAAC 57.211 29.630 0.00 0.00 39.17 2.93
2795 3674 9.262358 GTGTTCTAAGTTTTTCTGTATGAGAGT 57.738 33.333 0.00 0.00 30.18 3.24
2796 3675 9.261180 TGTGTTCTAAGTTTTTCTGTATGAGAG 57.739 33.333 0.00 0.00 30.18 3.20
2798 3677 9.817365 CATGTGTTCTAAGTTTTTCTGTATGAG 57.183 33.333 0.00 0.00 0.00 2.90
2814 3693 7.812191 GCCATGTTGTAAATTTCATGTGTTCTA 59.188 33.333 13.52 0.00 36.81 2.10
2822 3706 4.877251 GGCATGCCATGTTGTAAATTTCAT 59.123 37.500 32.08 0.00 35.81 2.57
2825 3709 3.263937 AGGGCATGCCATGTTGTAAATTT 59.736 39.130 36.56 0.00 37.98 1.82
2833 3717 1.496001 TCATCTAGGGCATGCCATGTT 59.504 47.619 36.56 20.86 37.98 2.71
2839 3723 6.161381 CCAATTTTTATCATCTAGGGCATGC 58.839 40.000 9.90 9.90 0.00 4.06
2845 3729 6.161381 GGCATGCCAATTTTTATCATCTAGG 58.839 40.000 32.08 0.00 35.81 3.02
2846 3730 6.751157 TGGCATGCCAATTTTTATCATCTAG 58.249 36.000 36.95 0.00 44.12 2.43
2890 3776 2.104451 TGTTTCACAGCCATGCCAATTT 59.896 40.909 0.00 0.00 0.00 1.82
2896 3782 0.953727 TGTCTGTTTCACAGCCATGC 59.046 50.000 0.00 0.00 45.54 4.06
2910 3796 5.598416 TGTCTATTCCACTGGTATGTCTG 57.402 43.478 0.00 0.00 0.00 3.51
2915 3801 7.347222 TGTTTCCTATGTCTATTCCACTGGTAT 59.653 37.037 0.00 0.00 0.00 2.73
2922 3808 8.877864 AAATGTTGTTTCCTATGTCTATTCCA 57.122 30.769 0.00 0.00 0.00 3.53
2980 3869 6.787458 TCCCCATTAGATGTTCTTAGAGCATA 59.213 38.462 11.41 0.00 33.85 3.14
2981 3870 5.608437 TCCCCATTAGATGTTCTTAGAGCAT 59.392 40.000 11.26 11.26 36.26 3.79
2990 3879 3.825328 AGCATGTCCCCATTAGATGTTC 58.175 45.455 0.00 0.00 0.00 3.18
2996 3885 3.307059 GGTAGCTAGCATGTCCCCATTAG 60.307 52.174 18.83 0.00 0.00 1.73
3000 3889 0.031111 AGGTAGCTAGCATGTCCCCA 60.031 55.000 24.01 0.00 0.00 4.96


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.